pH dependance of a Na channel Sodium ion channels play an important role in electrical signaling in cells; as such they are the targets of many drugs, as well as naturally occurring toxins from plant and animal sources. Inhibition and/or improper functioning of these channels due to mutation can lead to disease. The passage of sodium ions through bacterial voltage-gated sodium ion channels are controlled by a selectivity filter (SF) comprised of four glutamate residues. While it is known that the protonation state of the SF residues can alter the ability to ferry sodium ions, the existence of multiple proton binding sites in these channels makes it challenging to interpret the results of mutagenesis/electrophysiological experiments. Molecular dynamics (MD) simulations at constant pH offer a way to study pH-dependent effects with atomic-level detail. Na channels exhibit a decrease in conductance with lowering of pH. The selectivity filter (SF) of bacterial Na channels consists of four glutamate residues. The protonation states in the SF has been shown to modulate the number of bound Na+ ions, and most likely the conductivity. We study the protonation states in the SF of a bacterial Na channel through molecular dynamics, free energy perturbation as well as constant pH simulations. The simulations show that the number of bound ions influences the protonation state of the SF. With 2 or 3 ions bound, at physiological pH, the SF is most likely in fully deprotonated state, and possibly also the singly protonated state. With 1 or 0 ions bound, the doubly protonated state can also get populated. We are currently investigating the pH dependence of conductance of a bacterial ion channel (NavMs) which is known to exhibit a decrease in conductance with lowering of pH. Ionic Strength Induced Protein-Protein Interactions Protein kinases are dynamic and can adopt many conformational states, including active, inactive, and intermediate states which can represent an array of structural features that distinguish the ability of the protein to bind other molecules. Revealing the transitions between the conformational states of protein complexes is critical for effective rational design, as it would allow deeper insights into the structure function properties. Improper signaling of the nuclear factor-B (NF-B) pathway plays a critical role in many inflammatory disease states including cancer, stroke, and viral infections. While the signaling pathways are known, how these molecular mechanisms respond to changes in the intracellular microenvironment such as pH, ionic strength, and temperature, remains elusive. Molecular dynamics simulations were used to investigate how mutations and the ionic strength affect dimerization of the protein assembly to probe the affinity for tyrosine and serine phosphorylation activation mechanisms. Intermolecular interactions, thermodynamic properties, and conformational changes were compared among the inactive, active, and null states of the kinase. Results suggest that the multimeric assembly mediates a global stability for the enzyme that influences the activity of IKK and offers insight into which activation mechanism is preferred. Kinesin walking mechanism from SGLD simulations. Kinesin belongs to a family of molecular motors characterized by unidirectional movement along microtubules from the center of a cell to its periphery. Kinesin converts the energy of ATP hydrolysis into stepping movement along microtubules, which supports several vital cellular functions including mitosis, meiosis, and the transport of cellular cargo. Because kinesin is a fundamental protein, further research on the topic will provide important information as to how it functions. Combined with low resolution electron microscopic images, self-guided Langevin dynamics simulations are performed to study molecular motion and conformational change of kinesin motor domain in water and binding with microtubule. SGLD enable simulation to reach the time scale required for conformational change to understand the role of ATP binding and interaction with microtubules. Through flexible fitting of two newly release cryo-EM maps, we derived atomic structures of the kinesin dimer-microtubule complexes in both two-head-bound and one-head bound states. To identify which head generating the cargo moving force, we designed atomic force simulations to examine the responses of the two heads to dragging forces. Our simulation results show the leading head can provide a necessary force to perform the power stroke while the trailing head cannot stand for even a 5pN dragging force. A structure comparison between two-head-bound and one-head bound states also supports the conclusion that the leading head is the source of the cargo moving force. Also, in this study, through molecular simulations and free energy calculations, we found that in aqueous solution, kinesin favors an extended form with its microtubule-binding interface (MTBI) motif unfolded, as seen in a recent x-ray structure of kinesin-8. The transition between the extended and compact forms, the structural differences of the leading and trailing heads, and atomic force simulations lead us to a completely new mechanism by which kinesin dimers walk on microtubules. Mechanism of degradation of Histatin 5 peptide by Secreted Aspartic Protease (SAPS) of C. Albicans: Candida Albicans is a fungal opportunistic pathogen that commonly colonizes mucosal surfaces. Histatin 5 (Hst-5) is a 24 residue peptide in human saliva that has strong antifungal activity against C. Albicans. However, the pathogen has Secreted Aspartic Protease (SAPS) enzyme as part of its defense mechanism that cleaves Histatin 5 in a Lys residue and mutation of Lys to either Arg leads to intact peptide. We are studying the mechanism of cleavage of this enzyme and the difference between wild type and the Arg mutant that leads to decreased activity of enzyme. Crystal structure of the enzyme is in complex with an inhibitor. In order to dock the peptide to active site of protein we have removed the inhibitor and ran MD simulation on the enzyme and then docked the peptide (Hst5) to the active site of SAPS. We are using replica exchange umbrella sampling (REUS) to obtain the binding free energy of the peptide by pulling the peptide from the active site to bulk water phase. It is shown that most aspartic protease enzymes such as HIV-1 nucleophilic attack of water molecule activated by Asp residue in enzyme initiates the formation of gem-diol intermediate state in the backbone of peptide which lead to its cleavage. The suitable structure for cleavage of peptide which involves a water molecule is obtained from REUS simulation. Next, we are going to use QM/MM with a high level DFT in Quantum level to investigate the mechanism of cleavage of the enzyme. Prediction of water/octanol partition coefficients for the SAMPL6 blind challenge, Part 2 The water-octanol partition coefficient, log P, is an important parameter for efficacy of drug-like small molecules and an important intermediate for estimating log D and membrane permeability. We used three different approaches for our predictions: classical molecular mechanics using off-the-shelf as well as re-optimized molecular models (MM), implicit-solvent quantum mechanics with different basis sets and different levels of theory (QM), and deep learning from online databases (ML). The results were satisfactory: the three methods predicted log P for 11 molecules with a mean absolute error of 0.7 (MM), 1.0 (QM), and 0.5 (ML) and an RMSE of 0.8 (MM), 1.1 (QM), and 0.6 (ML).